Methods for analyzing biological elements

Abstract

The present invention is in the field of bioinformatics, particularly as it pertains to determining the associations of biological elements. More specifically, the present invention relates to the determination of associations among a set of biological elements using methods capable of generating and sorting clusters of biological elements.

1 . A method of analyzing a set of DNA sequences comprising: 
 a) performing an all-versus-all comparison of said set;    b) applying a transitive clustering algorithm at a defined relatedness to said set using results of said comparison to produce one or more clusters;    c) repeating step b) one or more times at increasingly greater levels of relatedness;    d) sorting the DNA sequences in a hierarchy based on said clusters; and    e) displaying the sorted DNA sequences;    wherein said defined relatedness is a value derived from a member of the group consisting of percent identity percent similarity, e-value, bit score and fraction of query and hit.    
     
     
         2 - 11 . (canceled)  
     
     
         12 . A program storage device readable by a machine, tangibly embodying a program of instructions executable by a machine to perform method steps to analyze a set of DNA sequences comprising: 
 a) performing all-versus-all comparison of said set including parsing said sequences using software that substantially follows the steps of the public domain Perl script “parse-blast.pl”:    b) applying a transitive clustering algorithm at a defined relatedness to said set using results of said comparison to produce one or more clusters where said algorithm substantially follows the steps of the Perl script “yc_cluster_inc100.pl”;    c) repeating step b) one or more times at increasingly greater levels of relatedness;    d) sorting said DNA sequences in a hierarchy based on said clusters where said sorting substantially follows the steps of the Perl script “sort_table99.pl”, and    e) displaying the sorted DNA sequences using software that substantially follows the Perl script “clustergram99.pl”.    
     
     
         13 - 21 . (canceled)